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Maria Chikina, Ph.D. - Publications

Affiliations: 
2011 Princeton University, Princeton, NJ 
Area:
Bioinformatics Biology, Computer Science, Molecular Biology
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24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Hu M, Chikina M. InstaPrism: an R package for fast implementation of BayesPrism. Bioinformatics (Oxford, England). PMID 38970377 DOI: 10.1093/bioinformatics/btae440  0.62
2024 Hu M, Chikina M. Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods. Genome Biology. 25: 169. PMID 38956606 DOI: 10.1186/s13059-024-03292-w  0.613
2024 Zhang S, Heil BJ, Mao W, Chikina M, Greene CS, Heller EA. MousiPLIER: A Mouse Pathway-Level Information Extractor Model. Eneuro. PMID 38789274 DOI: 10.1523/ENEURO.0313-23.2024  0.541
2024 Crawford J, Chikina M, Greene CS. Optimizer's dilemma: optimization strongly influences model selection in transcriptomic prediction. Bioinformatics Advances. 4: vbae004. PMID 38282973 DOI: 10.1093/bioadv/vbae004  0.492
2023 Zhang S, Heil BJ, Mao W, Chikina M, Greene CS, Heller EA. MousiPLIER: A Mouse Pathway-Level Information Extractor Model. Biorxiv : the Preprint Server For Biology. PMID 37577575 DOI: 10.1101/2023.07.31.551386  0.538
2023 Mao W, Miller CM, Nair VD, Ge Y, Amper MAS, Cappuccio A, George MC, Goforth CW, Guevara K, Marjanovic N, Nudelman G, Pincas H, Ramos I, Sealfon RSG, Soares-Schanoski A, ... ... Chikina M, et al. A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation. Molecular Systems Biology. e11361. PMID 36919946 DOI: 10.15252/msb.202211361  0.515
2022 Cappuccio A, Chawla DG, Chen X, Rubenstein AB, Cheng WS, Mao W, Burke TW, Tsalik EL, Petzold E, Henao R, McClain MT, Woods CW, Chikina M, Troyanskaya OG, Sealfon SC, et al. Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature. Cell Systems. 13: 989-1001.e8. PMID 36549275 DOI: 10.1016/j.cels.2022.11.008  0.541
2022 Sauerwald N, Zhang Z, Ramos I, Nair VD, Soares-Schanoski A, Ge Y, Mao W, Alshammary H, Gonzalez-Reiche AS, van de Guchte A, Goforth CW, Lizewski RA, Lizewski SE, Amper MAS, Vasoya M, ... ... Chikina M, et al. Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection. Cell Systems. PMID 36323307 DOI: 10.1016/j.cels.2022.10.005  0.64
2022 Crawford J, Christensen BC, Chikina M, Greene CS. Widespread redundancy in -omics profiles of cancer mutation states. Genome Biology. 23: 137. PMID 35761387 DOI: 10.1186/s13059-022-02705-y  0.46
2020 Kowalczyk A, Partha R, Clark NL, Chikina M. Pan-mammalian analysis of molecular constraints underlying extended lifespan. Elife. 9. PMID 32043462 DOI: 10.7554/Elife.51089  0.307
2019 Buschur KL, Chikina M, Benos PV. Causal network perturbations for instance-specific analysis of single cell and disease samples. Bioinformatics (Oxford, England). PMID 31873725 DOI: 10.1093/Bioinformatics/Btz949  0.302
2019 Raza Q, Choi JY, Li Y, O'Dowd RM, Watkins SC, Chikina M, Hong Y, Clark NL, Kwiatkowski AV. Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila. Plos Genetics. 15: e1007720. PMID 30763317 DOI: 10.1371/Journal.Pgen.1007720  0.301
2018 Tilstra JS, Avery L, Menk AV, Gordon RA, Smita S, Kane LP, Chikina M, Delgoffe GM, Shlomchik MJ. Kidney-infiltrating T cells in murine lupus nephritis are metabolically and functionally exhausted. The Journal of Clinical Investigation. PMID 30130253 DOI: 10.1172/Jci120859  0.303
2017 Zhang Q, Chikina M, Szymczak-Workman AL, Horne W, Kolls JK, Vignali KM, Normolle D, Bettini M, Workman CJ, Vignali DAA. LAG3 limits regulatory T cell proliferation and function in autoimmune diabetes. Science Immunology. 2. PMID 28783703 DOI: 10.1126/Sciimmunol.Aah4569  0.319
2016 Choi SG, Wang Q, Jia J, Chikina M, Pincas H, Dolios G, Sasaki K, Wang R, Minamino N, Salton SR, Sealfon SC. Characterization of gonadotrope secretoproteome identifies neurosecretory protein VGF-derived peptide suppression of follicle-stimulating hormone gene expression. The Journal of Biological Chemistry. PMID 27466366 DOI: 10.1074/Jbc.M116.740365  0.308
2016 Chikina M, Robinson JD, Clark NL. Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Molecular Biology and Evolution. PMID 27329977 DOI: 10.1093/Molbev/Msw112  0.319
2016 Weisel FJ, Zuccarino-Catania GV, Chikina M, Shlomchik MJ. A Temporal Switch in the Germinal Center Determines Differential Output of Memory B and Plasma Cells. Immunity. 44: 116-30. PMID 26795247 DOI: 10.1016/J.Immuni.2015.12.004  0.309
2015 Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, et al. A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 26447924 DOI: 10.1002/Cyto.A.22732  0.306
2015 Chikina MD, Gerald CP, Li X, Ge Y, Pincas H, Nair VD, Wong AK, Krishnan A, Troyanskaya OG, Raymond D, Saunders-Pullman R, Bressman SB, Yue Z, Sealfon SC. Low-variance RNAs identify Parkinson's disease molecular signature in blood. Movement Disorders : Official Journal of the Movement Disorder Society. 30: 813-21. PMID 25786808 DOI: 10.1002/Mds.26205  0.66
2012 Nair VD, Ge Y, Balasubramaniyan N, Kim J, Okawa Y, Chikina M, Troyanskaya O, Sealfon SC. Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells. Molecular and Cellular Biology. 32: 4861-76. PMID 23028048 DOI: 10.1128/Mcb.00816-12  0.56
2012 Chikina MD, Troyanskaya OG. An effective statistical evaluation of ChIPseq dataset similarity. Bioinformatics (Oxford, England). 28: 607-13. PMID 22262674 DOI: 10.1093/Bioinformatics/Bts009  0.48
2011 Chikina MD, Troyanskaya OG. Accurate quantification of functional analogy among close homologs. Plos Computational Biology. 7: e1001074. PMID 21304936 DOI: 10.1371/Journal.Pcbi.1001074  0.511
2009 Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. Plos Computational Biology. 5: e1000417. PMID 19543383 DOI: 10.1371/Journal.Pcbi.1000417  0.597
2008 Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG. The Sleipnir library for computational functional genomics. Bioinformatics (Oxford, England). 24: 1559-61. PMID 18499696 DOI: 10.1093/Bioinformatics/Btn237  0.587
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